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Doctor of Philosophy in Interdisciplinary Studies: Specialization in Bioinformatics

Degree Awarded: Ph.D.
Unit: IS
Program Webpage:

Program Information

Program Executive Committee Chair

Dr. Eric C. Rouchka, (502) 852-3060, Email Dr. Rouchka

General Information

The Interdisciplinary Ph.D. Program in Bioinformatics (the Bioinformatics Program) trains students in bioinformatics for careers in research, education, and industry.
Defined as “the field of science in which biology, computer science, and information technology merge to form a single discipline, bioinformatics is a broad and diverse domain, ranging from management of biological research databases to computational approaches to biomedical modeling and data analysis.
The Bioinformatics Program focuses on those aspects of bioinformatics that reflect the research interests and experience of the Program’s faculty.  These include basic research in biostatistical methodology, computer science and mathematical modeling with applications to biochemistry, cell biology and molecular biology.  The following areas have been identified and named by the Bioinformatics Program faculty to represent the focus application areas of the Program:
  • Biomedical and Natural Sciences
  • Computational Sciences
  • Mathematics and Statistics

Students in the Bioinformatics Program specialize in one of the three focus application areas and graduate with cutting-edge expertise in this area and working knowledge in the other two focus application areas. 


Graduate Studies -- Ph.D.

To earn the Doctor of Philosophy in Interdisciplinary Studies: Concentration in Bioinformatics, a student is required to successfully complete the following:

  • Core coursework in the focus application areas

  • Required coursework in the student’s area of specialization

  • Elective courses in the student’s area of specialization

  • Qualifying examination

  • Dissertation

  • Presentation and defense of dissertation

Good standing requires that the student maintain a minimum 3.0 grade point average.Upon successful completion of the written and oral portions of the qualifying examination, the examination committee will recommend acceptance into Ph.D. candidacy. Successful completion of the dissertation and its presentation and defense is established by the approval of the student’s dissertation committee and the approval of the chair of the sponsoring department and the program chair.

Programs of Study

Course requirements for the Interdisciplinary Ph.D. Degree Program in Bioinformatics consist of 16 core credit hours (that will be conditional based upon focus area) and 21 credit hours derived from a combination of required courses from a chosen focus area and electives from each of the three focus areas. Students with an appropriate background in the biomedical and natural sciences may petition to substitute a course in either the Computational Sciences or Mathematics and Statistics focus for the core course BIOC 545 Biochemistry I, and a corresponding course in either the Computational Sciences or Mathematics and Statistics for MBIO 667 Graduate Cell Biology, thus maintaining 16 core credit hours.   Following acceptance into a focus area, students will be required to complete three courses totaling at least nine hours from the declared focus area.  At least four additional elective courses (12 credit hours) will be selected from available elective courses, with the provision that two elective courses must be selected in each of the other two focus areas.  The Program of Study will be determined by the student and approved by both an advisor residing in a declared focus area department and the Executive Committee.  The following tables list the required courses for the core as well as the required and elective courses in each of the focus areas.  Students must accumulate at least nine credit hours of dissertation.

Core Course Work

Course Description
BIOC 545* Biochemistry I
BIOC 630* Responsible Conduct of Research: Survival Skills and Research Ethics
MBIO 667* Graduate Cell Biology
571/609# Computational Cognitive Science I 
CECS 660* Introduction to Bioinformatics
PHBI 750*
Statistical Methods for Bioinformatics

*All courses are required.  CHEM 645 may be substituted.  Students may take either the BIOC 545/BIOC547 or CHEM 645/647 sequence but are not allowed to take the sequence BIOC 545/CHEM647 or CHEM 645/BIOC547.  #Cross-listed as CECS 590-02.

Courses in Mathematics and Statistics

Department Course Description Credits
MATH 505 Introduction to Partial Differential Equations 3
MATH 507 Fourier Series 3
MATH 561# Probability 3
PHYS 565 Computational Physics 3
MATH 566 Nonparametric Statistical Methods 3
PHYS 625 Statistical Mechanics 3
PHST 630 Applied Statistical Models 3
MATH 636 Mathematical Modeling II 3
660 Probability Theory 3
661# Probability 3
PHST 662# Mathematical Statistics 3


562/662# Advanced Mathematical Statistics 3
MATH 665 Advanced Linear Statistical Models 3
MATH 667* Methods of Classification 3
MATH 670 Introduction to Stochastic Calculus 3
MATH 681 Combinatorics and Graph Theory I 3
MATH 682 Combinatorics and Graph Theory II 3
PHST 682 Multivariate Statistical Analysis 3
PHST 691 Bayesian Inference and Decision 3
PHST 710 Advanced Statistical Computing 3
PHST 711 Advanced Statistical Computing II
PHST 725 Design of Experiments 3
PHBI 751 High-throughput Data Analysis 3
PHBI 752 Statistical Genetics 3
PHST 762 Advanced Statistical Inference 3
PHST 780 Advanced Nonparametric Statistics
PHST 781 Advanced Linear Models 3
PHST 782 Generalized Linear Models

#Credit only for one: MATH 561/PHST 661; MATH 562/PHST 662

Courses in Biomedical and Natural Sciences

Department Course Description Credits
BIOL 542 Gene Structure and Function 3
BIOL 569 Evolution 3
BIOC 680 Biomolecular Interactions 3
BIOC 611 Biochemical and Molecular Methods 4
ASNB 614 Molecular Neuroscience 4
BIOC 641 Advanced Eukaryotic Genetics 3
BIOC 647# Advanced Biochemistry II 4
CHEM 647 Advanced Biochemistry II 4
CHEM 648 Systems Biochemistry Principles and Practices 3
CHEM 652 Practical Approaches to Metabolomics 3
BIOC 661 Molecular Mechanisms of Toxicology 3
BIOC 668 Molecular Biology 3
BIOC 670 Protein Structure and Function 4
CHEM 684 Biophysical Chemistry 3

#Credit only for one: CHEM 645/BIOC 645, CHEM 647/BIOC 647.  Students may take either the BIOC 545/BIOC547 or CHEM 645/647 sequence but are not allowed to take the sequence BIOC 545/CHEM647 or CHEM 645/BIOC547.

Courses in Computational Sciences

Department Course Description Credits
CECS 535 Introduction to Databases 3
CECS 546 Knowledge Engineering and Expert Systems 3
CECS 619 Design and Analysis of Computer Algorithms 3
CECS 622 Simulation and Modeling of Discrete Engineering Systems 3
CECS 624 Advanced Simulation 3
CECS 627 Digital Image Processing 3
CECS 628 Computer Graphics 3
CECS 629 Distributed System Design 3
CECS 630 Advanced Databases and Data Warehousing 3
CECS 632 Data Mining 3
CECS 641 Introduction to Medical Imaging 3
CECS 643 Introduction to Biomedical Computing 3
CECS 645 Advanced Artificial Intelligence 3
CECS 646 Intelligent Systems 3

Departmental Faculty

Participating Faculty for the Bioinformatics Program have primary appointments in various departments across the University, including:

  • College of Arts and Sciences: Departments of Biology, Chemistry, Mathematics, and Psychological and Brian Sciences
  • J.B. Speed School of Engineering: Department of Computer Engineering and Computer Science
  • School of Medicine: Departments of Anatomical Sciences and Neurobiology and Biochemistry and Molecular Biology
  • School of Public Health and Information Sciences: Departments of Bioinformatics and Biostatistics, Environmental Health and Occupational Health Sciences, and Epidemiology and Population Health


Eric C. Rouchka, Executive Committee Chair
D.Sc., Washington University in St. Louis
Associate Professor, Computer Engineering and Computer Science
Theodore S. Kalbfleisch, Executive Committee Vice-Chair
Ph.D., Boston University
Assistant Professor, Biochemistry and Molecular Biology
Guy Brock
Ph.D., University of New Mexico
Assistant Professor, Bioinformatics and Biostatistics
Nigel G.F. Cooper
Ph.D., University of Tennessee Health Sciences Center
Professor, Anatomical Sciences and Neurobiology
Somnath Datta
Ph.D., Michigan State University
Professor, Bioinformatics and Biostatistics
Susmita Datta
Ph.D., University of Georgia
Professor, Bioinformatics and Biostatistics
Ryan Gill
Ph.D., The University of Texas at Dallas
Associate Professor, Mathematics
Gary Hoyle
Ph.D., Duke University
Professor, Environmental and Occupational Health Sciences
Richard Kerber
Ph.D., Northwestern University
Associate Professor, Epidemiology and Population Health
Seongho Kim
Ph.D., Korea Advanced Institute of Science and Technology
Assistant Professor, Bioinformatics and Biostatistics
Jiaxu Li
Ph.D., Arizona State University
Assistant Professor, Mathematics
Hunter Moseley
Ph.D., University of Alabama at Birmingham
Assistant Professor, Chemistry
Rachel Neal
Ph.D., University of Missouri-Rolla
Assistant Professor, Environmental and Occupational Health Sciences
Liz O'Brien
Ph.D., Northwestern University
Assistant Professor, Epidemiology and Population Health
Ming Ouyang
Ph.D., Rutgers University
Assistant Professor, Computer Engineering and Computer Science
Michael Perlin
Ph.D., University of Chicago
Professor, Biology
Jeffrey C. Petruska
Ph.D., University of Florida
Assistant Professor, Anatomical Sciences and Neurobiology
Patrick Shafto
Ph.D., Northeastern University
Assistant Professor, Psychological and Brain Science
David Schultz
Ph.D., Pennsylvania State University
Associate Professor, Biology
Xiang Zhang
Ph.D., Purdue University
Associate Professor, Chemistry


Contact Information

Bioinformatics - Ph.D.

Eric Rouchka
University of Louisville Bioinformatics
Department of Anatomical Sciences and Neurobiology
Health Science Center, Building A, Room 916
500 South Preston Street
Louisville, Kentucky USA 40292 [Overnight zip code: 40202]
Phone: (502)852-3060
Fax: (502)852-3028

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